Compute properties (energy/forces) on series of geometries

aiida_nanotech_empa/workflows/cp2k/__init__.py

@@ -10,6 +10,7 @@
 from .orbitals_workchain import Cp2kOrbitalsWorkChain
 from .pdos_workchain import Cp2kPdosWorkChain
 from .phonons_workchain import Cp2kPhononsWorkChain
+from .reftraj_md_workchain import Cp2kRefTrajWorkChain
 from .replica_workchain import Cp2kReplicaWorkChain
 from .stm_workchain import Cp2kStmWorkChain
 
@@ -28,4 +29,5 @@
     "Cp2kReplicaWorkChain",
     "Cp2kNebWorkChain",
     "Cp2kPhononsWorkChain",
+    "Cp2kRefTrajWorkChain",
 )

aiida_nanotech_empa/workflows/cp2k/cp2k_utils.py

@@ -69,7 +69,14 @@ def get_kinds_section(kinds_dict, protocol="gapw_std"):
 
 def determine_kinds(structure, magnetization_per_site=None, ghost_per_site=None):
     """Gather the same atoms with the same magnetization into one atomic kind."""
-    ase_structure = structure.get_ase()
+
+    if isinstance(structure, orm.TrajectoryData):
+        cell = structure.get_array("cells")[0]
+        positions = structure.get_array("positions")[0]
+        symbols = structure.symbols
+        ase_structure = ase.Atoms(symbols, positions=positions, cell=cell)
+    else:
+        ase_structure = structure.get_ase()
 
     if magnetization_per_site is None or len(magnetization_per_site) == 0:
         magnetization_per_site = [0 for i in range(len(ase_structure))]
@@ -176,7 +183,6 @@ def load_protocol(fname, protocol=None):
 
 
 def get_dft_inputs(dft_params, structure, template, protocol):
-    ase_atoms = structure.get_ase()
     files = {
         "basis": orm.SinglefileData(
             file=os.path.join(
@@ -196,6 +202,18 @@ def get_dft_inputs(dft_params, structure, template, protocol):
         ),
     }
 
+    # number of atoms
+    if isinstance(structure, orm.TrajectoryData):
+        natoms = structure.get_shape("positions")[1]
+        structure = orm.StructureData(
+            ase=ase.Atoms(
+                structure.symbols,
+                positions=structure.get_array("positions")[0],
+                cell=(structure.get_array("cells")[0]),
+            )
+        )
+    natoms = len(structure.sites)
+
     # Load input template.
     input_dict = load_protocol(template, protocol)
 
@@ -211,7 +229,7 @@ def get_dft_inputs(dft_params, structure, template, protocol):
         input_dict["FORCE_EVAL"]["DFT"]["CHARGE"] = dft_params["charge"]
 
     # uks
-    magnetization_per_site = [0 for i in range(len(ase_atoms))]
+    magnetization_per_site = [0 for i in range(natoms)]
     if "uks" in dft_params:
         if dft_params["uks"]:
             magnetization_per_site = dft_params["magnetization_per_site"]

aiida_nanotech_empa/workflows/cp2k/protocols/md_reftraj_protocol.yml

@@ -0,0 +1,249 @@
+standard:
+    GLOBAL:
+        EXTENDED_FFT_LENGTHS: ''
+        PRINT_LEVEL: MEDIUM
+        RUN_TYPE: MD
+        WALLTIME: '600'
+        ELPA_KERNEL: AVX2_BLOCK2
+    MOTION:
+        MD:
+            STEPS: '1'
+            ENSEMBLE: 'REFTRAJ'
+            REFTRAJ:
+                FIRST_SNAPSHOT: '1'
+                LAST_SNAPSHOT: '1'
+                STRIDE: '1'
+                EVAL_FORCES: '.TRUE.'
+                TRAJ_FILE_NAME: 'aiida-reftraj.xyz'
+                VARIABLE_VOLUME: .TRUE.
+                CELL_FILE_NAME: 'aiida-reftraj.cell'
+        PRINT:
+            RESTART_HISTORY:
+                _: 'OFF'
+            FORCES:
+                EACH:
+                    MD: '1'
+                FORMAT: 'XYZ'
+            CELL:
+                EACH:
+                    MD: '1'
+    FORCE_EVAL:
+        METHOD: Quickstep
+        SUBSYS:
+            CELL:
+                PERIODIC: XYZ
+                SYMMETRY: ORTHORHOMBIC
+        DFT:
+            UKS: .FALSE.
+            MULTIPLICITY: '0'
+            CHARGE: '0'
+            BASIS_SET_FILE_NAME: BASIS_MOLOPT
+            POTENTIAL_FILE_NAME: POTENTIAL
+            RESTART_FILE_NAME: ./parent_calc/aiida-RESTART.wfn
+            MGRID:
+                CUTOFF: '600'
+                NGRIDS: '5'
+            POISSON:
+                PERIODIC: XYZ
+                POISSON_SOLVER: PERIODIC
+            QS:
+                EPS_DEFAULT: '1.0E-14'
+                EXTRAPOLATION: ASPC
+                EXTRAPOLATION_ORDER: '3'
+                METHOD: GPW
+            SCF:
+                SCF_GUESS: RESTART
+                EPS_SCF: '1.0E-7'
+                MAX_SCF: '40'
+                OT:
+                    MINIMIZER: CG
+                    PRECONDITIONER: FULL_SINGLE_INVERSE
+                OUTER_SCF:
+                    EPS_SCF: '1.0E-7'
+                    MAX_SCF: '50'
+                PRINT:
+                    RESTART:
+                        ADD_LAST: NUMERIC
+                        EACH:
+                            MD: '1'
+                        FILENAME: RESTART
+                    RESTART_HISTORY:
+                        _: 'OFF'
+                        BACKUP_COPIES: '0'
+            XC:
+                VDW_POTENTIAL:
+                    DISPERSION_FUNCTIONAL: PAIR_POTENTIAL
+                    PAIR_POTENTIAL:
+                        CALCULATE_C9_TERM: .TRUE.
+                        PARAMETER_FILE_NAME: dftd3.dat
+                        REFERENCE_FUNCTIONAL: PBE
+                        R_CUTOFF: '15'
+                        TYPE: DFTD3
+                XC_FUNCTIONAL:
+                        _: PBE
+low_accuracy:
+    GLOBAL:
+        EXTENDED_FFT_LENGTHS: ''
+        PRINT_LEVEL: MEDIUM
+        RUN_TYPE: MD
+        WALLTIME: '600'
+        ELPA_KERNEL: AVX2_BLOCK2
+    MOTION:
+        MD:
+            STEPS: '1'
+            ENSEMBLE: 'REFTRAJ'
+            REFTRAJ:
+                FIRST_SNAPSHOT: '1'
+                LAST_SNAPSHOT: '1'
+                STRIDE: '1'
+                EVAL_FORCES: '.TRUE.'
+                TRAJ_FILE_NAME: 'aiida-refttraj.xyz'
+                VARIABLE_VOLUME: .TRUE.
+                CELL_FILE_NAME: 'aiida-reftraj.cell'
+        PRINT:
+            RESTART_HISTORY:
+                _: 'OFF'
+            FORCES:
+                EACH:
+                    MD: '1'
+                FORMAT: 'XYZ'
+            CELL:
+                EACH:
+                    MD: '1'
+    FORCE_EVAL:
+        METHOD: Quickstep
+        SUBSYS:
+            CELL:
+                PERIODIC: XYZ
+                SYMMETRY: ORTHORHOMBIC
+        DFT:
+            UKS: .FALSE.
+            MULTIPLICITY: '0'
+            CHARGE: '0'
+            BASIS_SET_FILE_NAME: BASIS_MOLOPT
+            POTENTIAL_FILE_NAME: POTENTIAL
+            RESTART_FILE_NAME: ./parent_calc/aiida-RESTART.wfn
+            MGRID:
+                CUTOFF: '600'
+                NGRIDS: '5'
+            POISSON:
+                PERIODIC: XYZ
+                POISSON_SOLVER: PERIODIC
+            QS:
+                EPS_DEFAULT: '1.0E-14'
+                EXTRAPOLATION: ASPC
+                EXTRAPOLATION_ORDER: '3'
+                METHOD: GPW
+            SCF:
+                SCF_GUESS: RESTART
+                EPS_SCF: '1.0E-7'
+                MAX_SCF: '40'
+                OT:
+                    MINIMIZER: CG
+                    PRECONDITIONER: FULL_SINGLE_INVERSE
+                OUTER_SCF:
+                    EPS_SCF: '1.0E-7'
+                    MAX_SCF: '50'
+                PRINT:
+                    RESTART:
+                        ADD_LAST: NUMERIC
+                        EACH:
+                            MD: '1'
+                        FILENAME: RESTART
+                    RESTART_HISTORY:
+                        _: 'OFF'
+                        BACKUP_COPIES: '0'
+            XC:
+                VDW_POTENTIAL:
+                    DISPERSION_FUNCTIONAL: PAIR_POTENTIAL
+                    PAIR_POTENTIAL:
+                        CALCULATE_C9_TERM: .TRUE.
+                        PARAMETER_FILE_NAME: dftd3.dat
+                        REFERENCE_FUNCTIONAL: PBE
+                        R_CUTOFF: '15'
+                        TYPE: DFTD3
+                XC_FUNCTIONAL:
+                        _: PBE
+debug:
+    GLOBAL:
+        EXTENDED_FFT_LENGTHS: ''
+        PRINT_LEVEL: MEDIUM
+        RUN_TYPE: MD
+        WALLTIME: '600'
+        ELPA_KERNEL: AVX2_BLOCK2
+    MOTION:
+        MD:
+            STEPS: '1'
+            ENSEMBLE: 'REFTRAJ'
+            REFTRAJ:
+                FIRST_SNAPSHOT: '1'
+                LAST_SNAPSHOT: '1'
+                STRIDE: '1'
+                EVAL_FORCES: '.TRUE.'
+                TRAJ_FILE_NAME: 'aiida-reftraj.xyz'
+                VARIABLE_VOLUME: .TRUE.
+                CELL_FILE_NAME: 'aiida-reftraj.cell'
+        PRINT:
+            RESTART_HISTORY:
+                _: 'OFF'
+            FORCES:
+                EACH:
+                    MD: '1'
+                FORMAT: 'XYZ'
+            CELL:
+                EACH:
+                    MD: '1'
+    FORCE_EVAL:
+        METHOD: Quickstep
+        SUBSYS:
+            CELL:
+                PERIODIC: XYZ
+                SYMMETRY: ORTHORHOMBIC
+        DFT:
+            UKS: .FALSE.
+            MULTIPLICITY: '0'
+            CHARGE: '0'
+            BASIS_SET_FILE_NAME: BASIS_MOLOPT
+            POTENTIAL_FILE_NAME: POTENTIAL
+            RESTART_FILE_NAME: ./parent_calc/aiida-RESTART.wfn
+            MGRID:
+                CUTOFF: '600'
+                NGRIDS: '5'
+            POISSON:
+                PERIODIC: XYZ
+                POISSON_SOLVER: PERIODIC
+            QS:
+                EPS_DEFAULT: '1.0E-12'
+                EXTRAPOLATION: ASPC
+                EXTRAPOLATION_ORDER: '3'
+                METHOD: GPW
+            SCF:
+                SCF_GUESS: RESTART
+                EPS_SCF: '1.0E-1'
+                MAX_SCF: '40'
+                OT:
+                    MINIMIZER: CG
+                    PRECONDITIONER: FULL_SINGLE_INVERSE
+                OUTER_SCF:
+                    EPS_SCF: '1.0E-1'
+                    MAX_SCF: '50'
+                PRINT:
+                    RESTART:
+                        ADD_LAST: NUMERIC
+                        EACH:
+                            MD: '1'
+                        FILENAME: RESTART
+                    RESTART_HISTORY:
+                        _: 'OFF'
+                        BACKUP_COPIES: '0'
+            XC:
+                VDW_POTENTIAL:
+                    DISPERSION_FUNCTIONAL: PAIR_POTENTIAL
+                    PAIR_POTENTIAL:
+                        CALCULATE_C9_TERM: .TRUE.
+                        PARAMETER_FILE_NAME: dftd3.dat
+                        REFERENCE_FUNCTIONAL: PBE
+                        R_CUTOFF: '15'
+                        TYPE: DFTD3
+                XC_FUNCTIONAL:
+                        _: PBE